Contacts of the strand formed by residues 64 - 72 (chain B) in PDB entry 3F9C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PRO 3.9 2.0 + - - -
63B TYR* 1.3 74.6 - - - +
65B VAL* 1.3 55.7 + - - +
86B PRO* 3.3 8.7 - - - +
87B SER* 2.7 52.3 + - - -
88B GLN 4.5 4.3 + - - -
89B ASP 4.0 9.2 - - - -
90B ASN* 4.0 21.6 + - - +
133B ASN* 5.2 1.3 - - - -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY* 5.2 1.3 - - - +
63B TYR 3.8 1.3 - - - +
64B SER* 1.3 74.2 - - - +
66B GLY* 1.3 65.8 + - - +
84B TYR* 4.3 3.1 - - + -
85B TYR 3.4 1.8 - - - -
87B SER* 3.3 4.3 - - - -
93B LEU* 5.4 1.3 - - - +
131B PRO 4.6 5.4 - - - +
132B ALA* 3.6 5.4 - - + -
133B ASN* 2.8 37.1 + - - +
165B ILE* 3.4 51.6 - - + +
168B ALA* 3.6 20.0 - - + -
169B SER* 3.5 26.5 - - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 1.3 78.3 - - - +
67B CYS* 1.3 62.0 + - - +
84B TYR* 3.5 5.2 - - - -
85B TYR* 2.9 45.2 + - - -
87B SER* 3.2 18.3 + - - -
132B ALA* 4.3 1.3 - - - -
133B ASN* 3.2 12.1 - - - -
136B SER* 4.3 0.4 - - - -
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Residues in contact with CYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLY* 1.3 74.4 - - - +
68B THR* 1.3 61.8 + - - +
82B ARG* 3.5 35.0 - - - -
83B LEU 3.1 11.9 - - - +
84B TYR* 3.7 12.8 - - + -
85B TYR* 3.4 5.5 + - - -
95B THR* 3.7 23.3 - - - +
132B ALA* 3.6 19.5 - - + -
133B ASN 3.0 6.5 + - - -
134B TRP* 3.2 8.2 - - - -
135B ASN 2.7 30.5 + - - -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B CYS* 1.3 73.7 - - - +
69B ASP* 1.3 78.5 + - - +
82B ARG* 3.5 4.3 - - - +
83B LEU* 2.9 40.7 + - + +
85B TYR* 3.7 11.0 - - + -
134B TRP* 3.8 9.2 - - - -
135B ASN* 2.6 27.6 + - - -
251B LEU* 4.3 4.5 - - - +
253B PHE* 3.6 25.4 - - + +
255B MET* 3.7 24.3 - - + +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR* 1.3 78.4 + - - +
70B LEU* 1.3 60.6 + - - +
80B PHE* 4.6 0.7 - - + -
81B LEU 3.5 3.1 - - - +
82B ARG* 3.0 42.9 + - - +
99B PRO* 5.1 0.7 - - - +
134B TRP* 3.6 9.3 - - + -
157B ARG* 2.9 39.0 + - - -
247B ASN* 3.2 17.9 + - - -
249B LEU* 3.7 21.5 - - + +
251B LEU* 3.5 15.1 - - + +
255B MET* 4.0 2.8 - - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B THR* 5.8 0.2 - - + -
69B ASP* 1.3 73.9 - - - +
71B MET* 1.3 61.6 + - - +
72B PHE* 4.4 4.0 - - + -
79B THR 3.7 1.6 - - - +
80B PHE* 3.4 5.2 - - - -
81B LEU* 2.9 57.0 + - + +
83B LEU* 6.1 2.0 - - + -
235B LEU* 3.9 28.0 - - + -
236B ILE* 5.5 5.4 - - + -
239B ILE* 4.1 13.7 - - + -
245B VAL* 4.1 14.1 - - + -
247B ASN* 3.6 25.6 - - + -
255B MET* 3.9 36.3 - - + -
258B LEU* 5.9 1.6 - - + -
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 1.3 71.3 - - - +
72B PHE* 1.3 63.5 + - - +
73B ASP 3.5 13.2 - - - +
74B HIS* 4.1 13.2 - - - +
79B THR 3.3 8.5 - - - +
80B PHE* 3.7 21.1 - - + -
180B ARG* 3.5 18.8 - - - +
188B TYR* 3.5 48.9 - - + +
189B TYR* 4.2 1.1 - - - -
190B PHE* 3.8 26.9 - - + -
246B LYS 3.9 0.3 - - - +
247B ASN* 2.9 10.5 + - - +
248B ALA* 2.9 33.1 + - + +
249B LEU* 4.1 13.8 - - + +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.1 4.5 - - + +
71B MET* 1.3 74.3 - - - +
73B ASP* 1.3 71.8 + - + +
78B GLY* 3.8 0.5 - - - -
79B THR* 2.9 36.2 + - - +
231B GLN* 4.8 1.4 + - - -
235B LEU* 3.6 33.0 - - + +
243B LYS* 3.8 32.3 - - - -
244B PRO 4.6 3.4 - - - -
245B VAL* 3.8 21.3 - - + -
246B LYS* 3.1 37.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il